I'm having trouble reading my vcf file with PyVCF. Any help would be useful the file I'm trying to read was created by vcf tools.
Here is the code:
vcf_reader = vcf.Reader(open('all.mergedSNPs.vcf','r'))
for rec in vcf_reader:
But I get this error
Traceback (most recent call last):
File "", line 1, in
File "/Library/Python/2.7/site-packages/PyVCF-0.6.0-py2.7-macosx-10.7-intel.egg/vcf/parser.py", line 443, in next
pos = int(row)
IndexError: list index out of range
Is there an extra trailing blank line in the file?
Can you try again with HEAD?
No response from OP and PR merged, closing